wgcna_pipeline {TOmicsVis}

WGCNA analysis pipeline for RNA-Seq.

Description

WGCNA analysis pipeline for RNA-Seq.

Usage

wgcna_pipeline(
  sample_gene,
  group_sample,
  R_cutofff = 0.85,
  max_block = 5000,
  min_module = 20,
  network_type = "unsigned",
  merge_cutoff = 0.15,
  cor_type = "pearson",
  na_color = "#cdcdcd",
  xlab_angle = 45,
  text_size = 0.7
)

Arguments

sample_gene

Dataframe: All genes in all samples expression dataframe of RNA-Seq (1st-col: Genes, 2nd-col~: Samples).

group_sample

Dataframe: Samples and groups for gene expression (1st-col: Samples, 2nd-col: Groups).

R_cutofff

Numeric: Rsquare cutoff. Default: 0.85, min: 0.00, max: 1.00.

max_block

Numeric: max block size. Default: 5000.

min_module

Numeric: min module gene number. Default: 20.

network_type

Character: network type. Default: "unsigned", options: "unsigned", "signed", "signed hybrid".

merge_cutoff

Numeric: merge modules cutoff. Default: 0.15.

cor_type

Character: correlation type. Default: "pearson", options: "pearson", "bicor".

na_color

Character: NA value color (color name or hex value). Default: "#cdcdcd".

xlab_angle

Numeric: X axis lable angle. Default: 45, min: 0, max: 360.

text_size

Numeric: cell text size. Default: 0.7, min: 0, max: NULL.

Value

WGCNA results in tempdir() directory of current session.

Author(s)

benben-miao

Examples

# 1. Library TOmicsVis package
library(TOmicsVis)

# 2. Use example dataset
data(gene_expression)
head(gene_expression)

data(samples_groups)
head(samples_groups)